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Crystal structure of a Cysteine Desulfurase from Thermococcus onnurineus NA1 in complex with alanine at 2.3 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.03 M MgCl2, 0.03 M CaCl2, 15% (v/v) glycerol, 15% (w/v) PEG 4000, 5mM L-alanine, 1mM PLP and 0.1 M Tris (base)/ Bicine pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.282 α = 90 b = 93.809 β = 90 c = 145.534 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-07-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.28 50 95.5 0.095 34.6 6.4 40955
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.32 100 0.38 5.3 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5B7S 2.28 49.4 38845 2040 95.9 0.185 0.183 0.1941 0.232 0.2353 RANDOM 43.09
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.25 4.47 -4.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.107 r_dihedral_angle_3_deg 20.714 r_dihedral_angle_4_deg 15.378 r_long_range_B_other 8.405 r_long_range_B_refined 8.404 r_dihedral_angle_1_deg 6.897 r_scangle_other 6.809 r_mcangle_it 4.91 r_mcangle_other 4.91 r_scbond_other 4.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.107 r_dihedral_angle_3_deg 20.714 r_dihedral_angle_4_deg 15.378 r_long_range_B_other 8.405 r_long_range_B_refined 8.404 r_dihedral_angle_1_deg 6.897 r_scangle_other 6.809 r_mcangle_it 4.91 r_mcangle_other 4.91 r_scbond_other 4.48 r_scbond_it 4.479 r_mcbond_it 3.452 r_mcbond_other 3.451 r_angle_refined_deg 2.03 r_angle_other_deg 1.246 r_chiral_restr 0.161 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6218 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing